Snakemake Report

Jobs 1

Input files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/{pool}/popscle/demuxlet/demuxletOUT.best

Output files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/{pool}/CombinedResults/demuxlet_results.txt

Code

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            singularity exec --bind {params.bind} {params.sif} awk 'BEGIN{{OFS=FS="\t"}}{{print $2,$3,$5,$13,$14,$19,$20}}' {input.demuxlet} |             singularity exec --bind {params.bind} {params.sif} sed "s/SNG/singlet/g" |             singularity exec --bind {params.bind} {params.sif} sed "s/DBL/doublet/g" |             singularity exec --bind {params.bind} {params.sif} sed "s/AMB/unassigned/g" |             singularity exec --bind {params.bind} {params.sif} awk 'BEGIN{{FS=OFS="	"}} $3=="doublet" {{$4="doublet"}}1' |             singularity exec --bind {params.bind} {params.sif} sed "s/NUM.SNPS/nSNP/g" |             singularity exec --bind {params.bind} {params.sif} sed "s/DROPLET.TYPE/DropletType/g" |             singularity exec --bind {params.bind} {params.sif} sed "s/singlet.BEST.GUESS/Assignment/g" |             singularity exec --bind {params.bind} {params.sif} sed "s/singlet.BEST.LLK/SingletLLK/g" |             singularity exec --bind {params.bind} {params.sif} sed "s/doublet.BEST.LLK/DoulbetLLK/g" |             singularity exec --bind {params.bind} {params.sif} sed "s/DIFF.LLK.singlet.doublet/DiffLLK/g" |             singularity exec --bind {params.bind} {params.sif} sed "1s/	/	demuxlet_/g" |             singularity exec --bind {params.bind} {params.sif} sed "s/BARCODE/Barcode/g" |             singularity exec --bind {params.bind} {params.sif} awk 'NR<2{{print $0;next}}{{print $0 | "sort -k1"}}'  > {output}

Jobs 1

Input files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/{pool}/popscle/pileup/pileup.var.gz
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2021_09_12_from_imputation/imputed_hg38_R2_0.3_MAF0.05_exons_sorted.vcf
at 0x7f3297270b70>
at 0x7f3297262400>

Output files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/{pool}/popscle/demuxlet/demuxletOUT.best

Code

        singularity exec --bind {params.bind} {params.sif} popscle demuxlet             --plp {params.pileup}             --vcf {input.snps}             --field {params.field}             --geno-error-offset {params.geno_error_offset}             --geno-error-coeff {params.geno_error_coeff}             --r2-info {params.r2_info}             --min-mac {params.min_mac}             --min-callrate {params.min_callrate}             --group-list {input.barcodes}             --sm-list {input.individuals}             --doublet-prior {params.doublet_prior}             --cap-BQ {params.cap_BQ}             --min-BQ {params.min_BQ}             --min-MQ {params.min_MQ}             --min-TD {params.min_TD}             --excl-flag {params.excl_flag}             --min-total {params.min_total}             --min-snp {params.min_snp}             --out {params.out}demuxletOUT 
        [[ -s {output} ]]
        echo $?

Jobs 1

Input files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2021_09_12_from_imputation/imputed_hg38_R2_0.3_MAF0.05_exons_sorted.vcf
at 0x7f3297270e18>
at 0x7f3297270ea0>
at 0x7f3297270d90>

Output files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/{pool}/popscle/pileup/pileup.var.gz

Code

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        singularity exec --bind {params.bind} {params.sif} popscle dsc-pileup             --sam {input.bam}             --tag-group {params.tag_group}             --tag-UMI {params.tag_UMI}             --sm-list {input.individuals}             --vcf {input.vcf}             --cap-BQ {params.cap_BQ}             --min-BQ {params.min_BQ}             --min-MQ {params.min_MQ}             --min-TD {params.min_TD}             --excl-flag {params.excl_flag}             --group-list {input.barcodes}             --min-total {params.min_total}             --min-snp {params.min_snp}             --out {params.out}

Jobs 1

Input files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/{pool}/souporcell/clusters.tsv

Output files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/{pool}/CombinedResults/souporcell_results.txt

Code

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        singularity exec --bind {params.bind} {params.sif} awk 'BEGIN{{OFS=FS="\t"}}{{print $1,$2,$3,$4,$5}}' {input.souporcell} |             singularity exec --bind {params.bind} {params.sif} awk 'BEGIN{{FS=OFS="	"}} $2=="doublet" {{$3="doublet"}}1' |             singularity exec --bind {params.bind} {params.sif} awk 'BEGIN{{FS=OFS="	"}} $2=="unassigned" {{$4="unassigned"}}1' |             singularity exec --bind {params.bind} {params.sif} sed "s/status/DropletType/g" | sed "s/assignment/Assignment/g" |             singularity exec --bind {params.bind} {params.sif} sed "s/log_prob_singleton/LogProbSinglet/g" |             singularity exec --bind {params.bind} {params.sif} sed "s/log_prob_doublet/LogProbDoublet/g" |             singularity exec --bind {params.bind} {params.sif} sed "s/barcode/Barcode/g" |             singularity exec --bind {params.bind} {params.sif} sed "1s/	/	souporcell_/g" |             singularity exec --bind {params.bind} {params.sif} awk 'NR<2{{print $0;next}}{{print $0| "sort -k1"}}' > {output} 2> {log}

Jobs 1

Input files

at 0x7f329722f8c8>
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/{pool}/souporcell/barcodes.tsv
/directflow/SCCGGroupShare/projects/data/reference_data/1000G_hg38_imputation_ref/hg38/ref_genome_QC/Homo_sapiens.GRCh38.dna.primary_assembly.fa
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2021_09_12_from_imputation/imputed_hg38_R2_0.3_MAF0.05_exons_sorted.vcf

Output files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/{pool}/souporcell/clusters.tsv
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/{pool}/souporcell/cluster_genotypes.vcf
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/{pool}/souporcell/troublet.done
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/{pool}/souporcell/consensus.done
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/{pool}/souporcell/clustering.done

Code

        singularity exec --bind {params.bind} {params.sif} souporcell_pipeline.py             -i {input.bam}             -b {input.barcodes}             -f {input.fasta}             -t {threads}             -o {params.out}             -k {params.N}             --common_variants {input.snps}             --min_alt {params.min_alt}             --min_ref {params.min_ref}             --max_loci {params.max_loci} 2> {log}
        [[ -s {output.genotypes} ]]
        echo $?

Jobs 1

Input files

at 0x7f329722fd08>

Output files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/{pool}/souporcell/barcodes.tsv

Code

        if [[ {input.barcodes} == *".gz"* ]]
        then
            singularity exec --bind {params.bind} {params.sif} gunzip < {input.barcodes} > {output}
        else 
            singularity exec --bind {params.bind} {params.sif} cp {input.barcodes} {output}
        fi

Jobs 1

Input files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2021_09_12_from_imputation/imputed_hg38_R2_0.3_MAF0.05_exons_sorted.vcf
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/{pool}/souporcell/cluster_genotypes.vcf

Output files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/{pool}/souporcell/Individual_genotypes_subset.vcf.gz
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/{pool}/souporcell/Individual_genotypes_subset.vcf

Code

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        singularity exec --bind {params.bind} {params.sif} bedtools intersect -a {input.genotypes} -b {input.cluster_geno} -f 1.0 -r -wa -header > {output.filtered_refs_temp} 2> {log}
        singularity exec --bind {params.bind} {params.sif} bcftools view -S {params.individuals} -Oz -o {output.filtered_refs} {output.filtered_refs_temp} 2>> {log}

Jobs 1

Input files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/{pool}/scds/scds_doublets.txt

Output files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/{pool}/CombinedResults/scds_results.txt

Code

1 2	`awk 'NR<2{{print $0;next}}{{print $0\| "sort -k1,1"}}' {input} > {output}`

Jobs 1

Input files

at 0x7f32971f6ea0>

Output files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/{pool}/scds/scds_doublets.txt
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/{pool}/scds/scds_variables.txt

Code

        singularity exec --bind {params.bind} {params.sif} echo {wildcards.pool} > {output.variables}
        singularity exec --bind {params.bind} {params.sif} echo {params.out} >> {output.variables}
        singularity exec --bind {params.bind} {params.sif} echo {input.matrix_dir} >> {output.variables}
        singularity exec --bind {params.bind} {params.sif} Rscript {params.script} {output.variables}

Jobs 1

Input files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/Dropbox_files/TestData4PipelineSmall/samplesheet.txt

Output files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/manual_selections/scrublet/scrublet_percentile_manual_selection.tsv

Code

1 2	`singularity exec --bind {params.bind} {params.sif} awk 'BEGIN{{OFS=FS=" "}}{{print $1 " "}}' {input} \| sed "1s/.*/Pool scrublet_Percentile/" > {output} 2> {log}`

Jobs 1

Input files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/manual_selections/scrublet/scrublet_percentile_manual_selection.tsv
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/{pool}/scrublet_{pctl}/scrublet_results.txt

Output files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/{pool}/CombinedResults/{pctl}_scrublet_results.txt

Code

            if [ {params.ready} == "True" ]
            then 
                singularity exec --bind {params.bind} {params.sif} echo "Looks like you put percentile selections into the scrublet_gene_pctl.txt file." 2> {log}
                singularity exec --bind {params.bind} {params.sif} echo "The scrublet check is done and the next step of the pipeline will proceed" 2>> {log}
                singularity exec --bind {params.bind} {params.sif} awk 'NR<2{{print $0;next}}{{print $0| "sort -k1,1"}}' {input.results} > {output}
            elif [ {params.ready} == "False" ]
            then
                singularity exec --bind {params.bind} {params.sif} echo "You haven't put the scrublet gene percentile selection for each of the pools into the scrublet_gene_pctl.txt" 2> {log}
                singularity exec --bind {params.bind} {params.sif} echo "Please check the scrublet outputs and choose the best variable genes percentile - rerun any of the pools where the thresholding failed (see the docs) to choose a manual threshold"
                singularity exec --bind {params.bind} {params.sif} echo "Once you are happy with the thresholding, input the correct gene percentiles (as numbers between 0 and 100) into the second column of the scrublet_gene_pctl.txt file and restart the snakemake pipeline"
                singularity exec --bind {params.bind} {params.sif} echo 1
            fi

Jobs 1

Input files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/Dropbox_files/TestData4PipelineSmall/samplesheet.txt

Output files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/manual_selections/DoubletDetection/DoubletDetection_manual_selection.tsv

Code

1 2	`singularity exec --bind {params.bind} {params.sif} awk 'BEGIN{{OFS=FS=" "}}{{print $1 " "}}' {input} \| sed "1s/.*/Pool DoubletDetection_PASS_FAIL/" > {output} 2> {log}`

Jobs 1

Input files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/{pool}/DoubletDetection/DoubletDetection_results.txt
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/manual_selections/DoubletDetection/DoubletDetection_manual_selection.tsv

Output files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/{pool}/CombinedResults/DoubletDetection_results.txt

Code

            if [ {params.ready} == "True" ]
            then 
                singularity exec --bind {params.bind} {params.sif} echo "Looks like you put PASS into all the rows of DoubletDetection_manual_selection.tsv file." > {log}
                singularity exec --bind {params.bind} {params.sif} echo "The DoubletDetection check is done and the next step of the pipeline will proceed" >> {log}
                singularity exec --bind {params.bind} {params.sif} awk 'NR<2{{print $0;next}}{{print $0| "sort -k1,1"}}' {input.results} > {output}
            elif [ {params.ready} == "False" ]
            then
                singularity exec --bind {params.bind} {params.sif} echo "You haven't put PASS/FAIL values into the DoubletDetection_manual_selection.tsv file." > {log}
                singularity exec --bind {params.bind} {params.sif} echo "Please check the DoubletDetection outputs and decide if the pools passed - rerun any of the pools where the doublet numbers don't reach convergence using the manual selections (see the docs)" >> {log}
                singularity exec --bind {params.bind} {params.sif} echo "Once you are happy with the results, input PASS into the second column of the DoubletDetection_manual_selection.tsv file and restart the snakemake pipeline" >> {log}
                singularity exec --bind {params.bind} {params.sif} echo 1
            fi

Jobs 1

Input files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/{pool}/CombinedResults/CombinedDropletAssignments_w_genotypeIDs.tsv

Output files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/{pool}/CombinedResults/DropletType_Assignment_BarPlot.png
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/{pool}/CombinedResults/Final_Assignments_demultiplexing_doublets.txt
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/{pool}/CombinedResults/variables.txt

Code

        singularity exec --bind {params.bind} {params.sif} echo {params.out} > {output.variables}
        singularity exec --bind {params.bind} {params.sif} echo {wildcards.pool} >> {output.variables}
        singularity exec --bind {params.bind} {params.sif} Rscript {params.script} {output.variables}
        [[ -s {output.figure} ]]
        echo $?

Jobs 1

Input files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/{pool}/souporcell/Individual_genotypes_subset.vcf.gz
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/{pool}/CombinedResults/CombinedDropletAssignments.tsv

Output files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/{pool}/CombinedResults/CombinedDropletAssignments_w_genotypeIDs.tsv
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/{pool}/souporcell/souporcel_genotypes_variables
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/{pool}/souporcell/genotype_correlations/pearson_correlation.png

Code

        singularity exec --bind {params.bind} {params.sif} echo {params.out} > {output.variables}
        singularity exec --bind {params.bind} {params.sif} echo {wildcards.pool} >> {output.variables}
        singularity exec --bind {params.bind} {params.sif} echo {input.assignments} >> {output.variables}
        singularity exec --bind {params.bind} {params.sif} echo {params.cor_thresh} >> {output.variables}
        singularity exec --bind {params.bind} {params.sif} Rscript {params.script} {output.variables} 2> {log}
        [[ -s {output.assignments} ]]
        echo $?

Jobs 1

Input files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/{pool}/CombinedResults/demuxlet_results.txt
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/{pool}/CombinedResults/souporcell_results.txt
at 0x7f329721a1e0>
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/{pool}/CombinedResults/scds_results.txt
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/{pool}/CombinedResults/DoubletDetection_results.txt

Output files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/{pool}/CombinedResults/CombinedDropletAssignments.tsv

Code

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        join -a1 -a2 -1 1 -2 1 -t "	" -e"NA" -o "0,1.2,1.3,1.4,1.5,1.6,1.7,2.2,2.3,2.4,2.5" {input.demuxlet} {input.souporcell} | awk 'NR<2{{print $0;next}}{{print $0| "sort -k1"}}' |             join -a1 -a2 -1 1 -2 1 -t "	" -e"NA" -o "0,1.2,1.3,1.4,1.5,1.6,1.7,1.8,1.9,1.10,1.11,2.2,2.3" - {input.scrublet} | awk 'NR<2{{print $0;next}}{{print $0| "sort -k1"}}' |             join -a1 -a2 -1 1 -2 1 -t "	" -e"NA" -o "0,1.2,1.3,1.4,1.5,1.6,1.7,1.8,1.9,1.10,1.11,1.12,1.13,2.2,2.3" - {input.scds} | awk 'NR<2{{print $0;next}}{{print $0| "sort -k1"}}' |             join -a1 -a2 -1 1 -2 1 -t "	" -e"NA" -o "0,1.2,1.3,1.4,1.5,1.6,1.7,1.8,1.9,1.10,1.11,1.12,1.13,1.14,1.15,2.2" - {input.DoubletDetection} > {output}

Jobs 1

Input files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/QC_figures/final_assignments_comparison.txt
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/QC_figures/meta_comparison.txt

Output files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/QC_figures/R_variables.txt
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/QC_figures/nCount_RNA_violin_MAD_All.png
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/QC_figures/nCount_RNA_violin_MADper_Pool.png
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/QC_figures/nCount_RNA_violin_noMADlines.png
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/QC_figures/nFeature_RNA_violin_MAD_All.png
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/QC_figures/nFeature_RNA_violin_MADper_Pool.png
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/QC_figures/nFeature_RNA_violin_noMADlines.png
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/QC_figures/nFeatures_vs_percentMT_QC_scatter_colorPool.png
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/QC_figures/nFeatures_vs_percentMT_QC_scatter_w_MADlines.png
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/QC_figures/percent.mt_violin_MAD_All.png
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/QC_figures/percent.mt_violin_MADper_Pool.png
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/QC_figures/percent.mt_violin_noMADlines.png
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/QC_figures/percent.rb_violin_MAD_All.png
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/QC_figures/percent.rb_violin_MADper_Pool.png
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/QC_figures/percent.rb_violin_noMADlines.png
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/QC_figures/UMI_vs_Genes_QC_scatter.png
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/QC_figures/UMI_vs_Genes_QC_scatter_w_MADlines.png
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/QC_figures/UMI_vs_percentMT_QC_scatter_colorPool.png
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/QC_figures/UMI_vs_percentMT_QC_scatter_w_MADlines.png

Code

        singularity exec --bind {params.bind} {params.sif} echo {params.main_dir} > {output.variables}
        singularity exec --bind {params.bind} {params.sif} echo {input.pools} >> {output.variables}
        singularity exec --bind {params.bind} {params.sif} echo {params.dirs10x} >> {output.variables}
        singularity exec --bind {params.bind} {params.sif} echo {params.out} >> {output.variables}
        singularity exec --bind {params.bind} {params.sif} echo {params.rb_genes} >> {output.variables}
        singularity exec --bind {params.bind} {params.sif} echo {params.mt_genes} >> {output.variables}
        singularity exec --bind {params.bind} {params.sif} Rscript {params.script} {output.variables}
        [[ -s {output.fig18} ]]
        echo $?

Jobs 1

Input files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/QC_figures/final_assignments.txt
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/Dropbox_files/TestData4PipelineSmall/samplesheet.txt

Output files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/QC_figures/final_assignments_comparison.txt
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/QC_figures/meta_comparison.txt

Code

        singularity exec --bind {params.bind} {params.sif} cat {input.assignment_list} > {output.assignment_list}
        singularity exec --bind {params.bind} {params.sif} awk 'BEGIN{{FS=OFS="	"}}{{print $1}}' {input.meta} | singularity exec --bind {params.bind} {params.sif} tail -n+2 > {output.meta}
        if [ "$(wc -l < {output.meta})" -eq "$(wc -l < {output.assignment_list})" ]
        then 
            echo 0
        else 
            echo "The number of pools in the final_assignments.txt file don't match the number of pools in your sample sheet" > {log}
            rm {input.assignment_list}
            rm {output.assignment_list}
            rm {output.meta}
            echo 1
        fi

Jobs 1

Input files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/test_dataset/CombinedResults/Final_Assignments_demultiplexing_doublets.txt

Output files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/QC_figures/final_assignments.txt

Code

1
2
3

        singularity exec --bind {params.bind} {params.sif} echo {input} | singularity exec --bind {params.bind} {params.sif} tr ' ' '
' >> {output}

Jobs 1

Input files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/QC_figures/final_assignments.txt
/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/Dropbox_files/TestData4PipelineSmall/samplesheet.txt

Output files

/directflow/SCCGGroupShare/projects/DrewNeavin/Demultiplex_Benchmark/test_pipeline/demultiplexing/2022_03_04/results/QC_figures/expected_observed_individuals_classifications.png

Code

1 2	`singularity exec --bind {params.bind} {params.sif} Rscript {params.script} {input.sample_sheet} {params.out} {params.basedir}`

Workflow

DoubletDetection

test_dataset

Number Individuals Summary

QC

Scrublet

test_dataset

Souporcell Genotype Correlations

test_dataset

Statistics